Plant Circular RNA Database

Detail information of AT3G52140_circ_g.12

			
						 General Information
					
						CircRNA Name
						AT3G52140_circ_g.12
					
						ID in PlantcircBase
						ath_circ_027101
					
						Alias
						3:19336287-19338675
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 19336287-19338675  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G52140						
					
						Parent gene annotation
						
							Clustered mitochondria protein homolog
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G52140_circ_g.7 AT3G52140_circ_g.8 AT3G52140_circ_g.9 AT3G52140_circ_g.10 AT3G52140_circ_g.11 AT3G52140_circ_g.13 AT3G52140_circ_g.14 AT3G52140_circ_g.15 AT3G52140_circ_g.16 AT3G52140_circ_g.17 AT3G52140_circ_g.18 AT3G52140_circ_g.19 AT3G52140_circ_g.20 AT3G52140_circ_g.21 AT3G52140_circ_g.22 AT3G52140_circ_g.23 AT3G52140_circ_g.24 						
					
						Support reads
						2/1/1
					
						Tissues
						seedling;root
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						AT3G52140.1:8
AT3G52140.3:8
AT3G52140.4:8
AT3G52140.2:8

General Information
CircRNA Name	AT3G52140_circ_g.12
ID in PlantcircBase	ath_circ_027101
Alias	3:19336287-19338675
Organism	Arabidpsis thaliana
Position	chr3: 19336287-19338675 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G52140
Parent gene annotation	Clustered mitochondria protein homolog
Parent gene strand	+
Alternative splicing	AT3G52140_circ_g.7 AT3G52140_circ_g.8 AT3G52140_circ_g.9 AT3G52140_circ_g.10 AT3G52140_circ_g.11 AT3G52140_circ_g.13 AT3G52140_circ_g.14 AT3G52140_circ_g.15 AT3G52140_circ_g.16 AT3G52140_circ_g.17 AT3G52140_circ_g.18 AT3G52140_circ_g.19 AT3G52140_circ_g.20 AT3G52140_circ_g.21 AT3G52140_circ_g.22 AT3G52140_circ_g.23 AT3G52140_circ_g.24
Support reads	2/1/1
Tissues	seedling;root
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	AT3G52140.1:8 AT3G52140.3:8 AT3G52140.4:8 AT3G52140.2:8

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							ATCAGCAGTCTCACATTTCCTCAATTGTTTCTTTGGAAACTATCAAACTGCTGGGGGAAAAGCT
AGCGCCAACAGCTCTACTGCCAAAAATCAAAAGAAGgtatgtgcacaacaacatctttttcagt
tttgctgttgatgccgacattgaacagctctccaagaaacgtccatctaatcaaatgacggaga
aggtgtcc

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 1318
Transcript exons: 19336287-19336602,19336699-19336803,19336968-19337195,19
337267-19337407,19337872-19338006,19338097-19338267,1933
8347-19338433,19338541-19338675
GTATGTGCACAACAACATCTTTTTCAGTTTTGCTGTTGATGCCGACATTGAACAGCTCTCCAAG
AAACGTCCATCTAATCAAATGACGGAGAAGGTGTCCTCATCTGAAAAGGTTTCATGCACAGAAG
GAACCTGCGATAATGAAGAGCATAACAACTGTAATGAGGCGCCACTTGTTGAGAATGAGCAGGC
TACGTATGCCTCTGCAAACAATGATTTGAAAGGCACAAAATTATATCAAGAAGCTGATGTCCCA
GGGCTATATAATCTGGCAATGGCCATTATTGATTACAGAGGCCATAGGGTTGTTGCTCAGAGTG
TTCTACCGGGAATCCTTCAAGGGGATAAATCAGATGCGCTTTTGTACGGTTCAGTCGACAATGG
CAAGAAAATATGCTGGAATGAAGATTTTCATGCTAAGGTGCTAGAGGCCGCAAAGCTTCTTCAC
ATTAAGGAACATTCTGTTATCGATGCATCCGAAACTGTCTTTAAGTTGGCTGCACCAGTAGAGT
GCAAAGGGATTGTTGGGAGTGATAACAGGCATTATCTCTTGGACTTGATGAGAGTGACACCTCG
TGATGCCAATTATACGGGCCCAGAGTCACGCTTTTGTGTCCTAAGACCAGAACTGATCACATCA
TTTTGCCAGGCCGAATCATTGGAAAAATCAAAATTTAAAACCAAGGCTGATGAAGGGGGCGATG
ATTCTTCTAATGTTAGTGCTGATACTTCTAAAGTTGGTGATGCATTGATCGATGGAGAGGCAAA
TGGGGCTTCAAATTCTGATCAGAAATCTATTTCAGACAAGCAAAATACCACTGCCGAAGATTAT
GCAGCCGGGTCTTCTGAAAGTTCCAAATCATGTGATCAAATAGCATTTAACCCCAATGTCTTCA
CTGACTTCACATTAGGTGGCAATCAAGAGGAGATAGCTGCTGATGAAGAAAATGTGAAGAAAGT
TAGCTCATACCTTGTGGATGTGGTCCTTCCAAAGTTTATAGAAGATCTTTGCACTCTCGAAGTT
TCTCCAATGGATGGTCAGACTTTGACAGAAGCACTCCATGCTCATGGTGTTAATGTTCGTTACA
TTGGAAGAGTTGCTAATGGGGTGAAGCATTTGCCTCATTTGTGGGACCTTTGTCTGAATGAGAT
TACTGTAAGATCCGCAAAGCACATTTTGAAGGACATTCTAAGAGATATAGAGGATCACGATATT
GGATCAGCAGTCTCACATTTCCTCAATTGTTTCTTTGGAAACTATCAAACTGCTGGGGGAAAAG
CTAGCGCCAACAGCTCTACTGCCAAAAATCAAAAGAAG
						
					

						Genomic sequence
						
							GTATGTGCACAACAACATCTTTTTCAGTTTTGCTGTTGATGCCGACATTGAACAGCTCTCCAAG
AAACGTCCATCTAATCAAATGACGGAGAAGGTGTCCTCATCTGAAAAGGTTTCATGCACAGAAG
GAACCTGCGATAATGAAGAGCATAACAACTGTAATGAGGCGCCACTTGTTGAGAATGAGCAGGC
TACGTATGCCTCTGCAAACAATGATTTGAAAGGCACAAAATTATATCAAGAAGCTGATGTCCCA
GGGCTATATAATCTGGCAATGGCCATTATTGATTACAGAGGCCATAGGGTTGTTGCTCAGGTTT
GTTCAAATACTGGAACTTCCAAGTCCTTATTCTTGAGATTGTCTGTGTCTTGCTTGTGTTCATT
TTAATAGTATCTTTGCAATGTGTTTTAGAGTGTTCTACCGGGAATCCTTCAAGGGGATAAATCA
GATGCGCTTTTGTACGGTTCAGTCGACAATGGCAAGAAAATATGCTGGAATGAAGATTTTCATG
CTAAGGTAAATGAATATAGTCTCTTGCTGTTGGATACCGTAGGCATTAATGTGAAAATTCTAGT
AGTAATCTATCTGTACAATATTAATATTAATATTTATCTGTATACTATTATAAGACTGCACGTG
TCCTAGCAGAAATATTTGATCCTGATTAATTCCTTCTTCAGGTGCTAGAGGCCGCAAAGCTTCT
TCACATTAAGGAACATTCTGTTATCGATGCATCCGAAACTGTCTTTAAGTTGGCTGCACCAGTA
GAGTGCAAAGGGATTGTTGGGAGTGATAACAGGCATTATCTCTTGGACTTGATGAGAGTGACAC
CTCGTGATGCCAATTATACGGGCCCAGAGTCACGCTTTTGTGTCCTAAGACCAGAACTGATCAC
ATCATTTTGCCAGGTACATATTTTCTTTATTATTTAGAAAAGTATGCTCTTGAGTTCCATTGAC
AACTTATTTTCATCATGAAGGCCGAATCATTGGAAAAATCAAAATTTAAAACCAAGGCTGATGA
AGGGGGCGATGATTCTTCTAATGTTAGTGCTGATACTTCTAAAGTTGGTGATGCATTGATCGAT
GGAGAGGCAAATGGGGCTTCAAATTCTGATCAGGTATATGTTTCACTTTTTGATCCGGATAGAT
ATGTGCATTAAGCATATGTAGTACTGATTGACGTTTCTATTTCAACTGGGATTTGTATGAATAT
TTAGGAATTTACATCTGCTTGATATACCCTGCTTTTTGTGTTCAATGGCTGCTATTAGTTTATG
TGGATGCTGTGTCTCACTATCAGATTTTATAGACGTAGAATGTTTGTCAAATGAAAAGGCAGAC
TGACAAAAACCAAATAGGATATGGACCCTGTAACAATGATGGAAATAACAATTTTACTTGTACA
TTAGTAGATCTCTACTAAATTAATCAATTGGACTGGGTCTTGCTTGTTCATTCCTCTATTGTTT
TTGCTTTGAGATTCTTTTTCCCATCATTGCTTTCGACTGAATGGATAGAAATGTCTGATAACAG
TTGTATCTGAAAAAAACTGTAACTGCTGATATCTGCGTTTTCTTTACAGAAATCTATTTCAGAC
AAGCAAAATACCACTGCCGAAGATTATGCAGCCGGGTCTTCTGAAAGTTCCAAATCATGTGATC
AAATAGCATTTAACCCCAATGTCTTCACTGACTTCACATTAGGTGGCAATCAAGAGGTAGGTTA
TGTTGCTTATAGGTTATATGTTTTAAGATCATCTCTTAAAATTTATTTAACTGATTGGATGAAT
CCTTTTTGGGTTAAACAGGAGATAGCTGCTGATGAAGAAAATGTGAAGAAAGTTAGCTCATACC
TTGTGGATGTGGTCCTTCCAAAGTTTATAGAAGATCTTTGCACTCTCGAAGTTTCTCCAATGGA
TGGTCAGACTTTGACAGAAGCACTCCATGCTCATGGTGTTAATGTTCGTTACATTGGAAGAGTA
AGTTTGTCAGCTGTCGTTATCATTTTGTTAGCTATCTCTATGTTTGAGTTTATTAACAGTAGAT
TTGCTCGACCAGGTTGCTAATGGGGTGAAGCATTTGCCTCATTTGTGGGACCTTTGTCTGAATG
AGATTACTGTAAGATCCGCAAAGCACATTTTGAAGGTAATTTTGACTGTTGTAAAAGCATGCCA
CAACAAGAGTTAGGGTATCTGTGGACACGCTTGTAATAGGTTATAATGTTATTTCTATGTTCTT
ACGTCGTTGTGCAGGACATTCTAAGAGATATAGAGGATCACGATATTGGATCAGCAGTCTCACA
TTTCCTCAATTGTTTCTTTGGAAACTATCAAACTGCTGGGGGAAAAGCTAGCGCCAACAGCTCT
ACTGCCAAAAATCAAAAGAAG
						
					

			
		

Sequences
Splice junction sequence	ATCAGCAGTCTCACATTTCCTCAATTGTTTCTTTGGAAACTATCAAACTGCTGGGGGAAAAGCT AGCGCCAACAGCTCTACTGCCAAAAATCAAAAGAAGgtatgtgcacaacaacatctttttcagt tttgctgttgatgccgacattgaacagctctccaagaaacgtccatctaatcaaatgacggaga aggtgtcc
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 1318 Transcript exons: 19336287-19336602,19336699-19336803,19336968-19337195,19 337267-19337407,19337872-19338006,19338097-19338267,1933 8347-19338433,19338541-19338675 GTATGTGCACAACAACATCTTTTTCAGTTTTGCTGTTGATGCCGACATTGAACAGCTCTCCAAG AAACGTCCATCTAATCAAATGACGGAGAAGGTGTCCTCATCTGAAAAGGTTTCATGCACAGAAG GAACCTGCGATAATGAAGAGCATAACAACTGTAATGAGGCGCCACTTGTTGAGAATGAGCAGGC TACGTATGCCTCTGCAAACAATGATTTGAAAGGCACAAAATTATATCAAGAAGCTGATGTCCCA GGGCTATATAATCTGGCAATGGCCATTATTGATTACAGAGGCCATAGGGTTGTTGCTCAGAGTG TTCTACCGGGAATCCTTCAAGGGGATAAATCAGATGCGCTTTTGTACGGTTCAGTCGACAATGG CAAGAAAATATGCTGGAATGAAGATTTTCATGCTAAGGTGCTAGAGGCCGCAAAGCTTCTTCAC ATTAAGGAACATTCTGTTATCGATGCATCCGAAACTGTCTTTAAGTTGGCTGCACCAGTAGAGT GCAAAGGGATTGTTGGGAGTGATAACAGGCATTATCTCTTGGACTTGATGAGAGTGACACCTCG TGATGCCAATTATACGGGCCCAGAGTCACGCTTTTGTGTCCTAAGACCAGAACTGATCACATCA TTTTGCCAGGCCGAATCATTGGAAAAATCAAAATTTAAAACCAAGGCTGATGAAGGGGGCGATG ATTCTTCTAATGTTAGTGCTGATACTTCTAAAGTTGGTGATGCATTGATCGATGGAGAGGCAAA TGGGGCTTCAAATTCTGATCAGAAATCTATTTCAGACAAGCAAAATACCACTGCCGAAGATTAT GCAGCCGGGTCTTCTGAAAGTTCCAAATCATGTGATCAAATAGCATTTAACCCCAATGTCTTCA CTGACTTCACATTAGGTGGCAATCAAGAGGAGATAGCTGCTGATGAAGAAAATGTGAAGAAAGT TAGCTCATACCTTGTGGATGTGGTCCTTCCAAAGTTTATAGAAGATCTTTGCACTCTCGAAGTT TCTCCAATGGATGGTCAGACTTTGACAGAAGCACTCCATGCTCATGGTGTTAATGTTCGTTACA TTGGAAGAGTTGCTAATGGGGTGAAGCATTTGCCTCATTTGTGGGACCTTTGTCTGAATGAGAT TACTGTAAGATCCGCAAAGCACATTTTGAAGGACATTCTAAGAGATATAGAGGATCACGATATT GGATCAGCAGTCTCACATTTCCTCAATTGTTTCTTTGGAAACTATCAAACTGCTGGGGGAAAAG CTAGCGCCAACAGCTCTACTGCCAAAAATCAAAAGAAG
Genomic sequence	GTATGTGCACAACAACATCTTTTTCAGTTTTGCTGTTGATGCCGACATTGAACAGCTCTCCAAG AAACGTCCATCTAATCAAATGACGGAGAAGGTGTCCTCATCTGAAAAGGTTTCATGCACAGAAG GAACCTGCGATAATGAAGAGCATAACAACTGTAATGAGGCGCCACTTGTTGAGAATGAGCAGGC TACGTATGCCTCTGCAAACAATGATTTGAAAGGCACAAAATTATATCAAGAAGCTGATGTCCCA GGGCTATATAATCTGGCAATGGCCATTATTGATTACAGAGGCCATAGGGTTGTTGCTCAGGTTT GTTCAAATACTGGAACTTCCAAGTCCTTATTCTTGAGATTGTCTGTGTCTTGCTTGTGTTCATT TTAATAGTATCTTTGCAATGTGTTTTAGAGTGTTCTACCGGGAATCCTTCAAGGGGATAAATCA GATGCGCTTTTGTACGGTTCAGTCGACAATGGCAAGAAAATATGCTGGAATGAAGATTTTCATG CTAAGGTAAATGAATATAGTCTCTTGCTGTTGGATACCGTAGGCATTAATGTGAAAATTCTAGT AGTAATCTATCTGTACAATATTAATATTAATATTTATCTGTATACTATTATAAGACTGCACGTG TCCTAGCAGAAATATTTGATCCTGATTAATTCCTTCTTCAGGTGCTAGAGGCCGCAAAGCTTCT TCACATTAAGGAACATTCTGTTATCGATGCATCCGAAACTGTCTTTAAGTTGGCTGCACCAGTA GAGTGCAAAGGGATTGTTGGGAGTGATAACAGGCATTATCTCTTGGACTTGATGAGAGTGACAC CTCGTGATGCCAATTATACGGGCCCAGAGTCACGCTTTTGTGTCCTAAGACCAGAACTGATCAC ATCATTTTGCCAGGTACATATTTTCTTTATTATTTAGAAAAGTATGCTCTTGAGTTCCATTGAC AACTTATTTTCATCATGAAGGCCGAATCATTGGAAAAATCAAAATTTAAAACCAAGGCTGATGA AGGGGGCGATGATTCTTCTAATGTTAGTGCTGATACTTCTAAAGTTGGTGATGCATTGATCGAT GGAGAGGCAAATGGGGCTTCAAATTCTGATCAGGTATATGTTTCACTTTTTGATCCGGATAGAT ATGTGCATTAAGCATATGTAGTACTGATTGACGTTTCTATTTCAACTGGGATTTGTATGAATAT TTAGGAATTTACATCTGCTTGATATACCCTGCTTTTTGTGTTCAATGGCTGCTATTAGTTTATG TGGATGCTGTGTCTCACTATCAGATTTTATAGACGTAGAATGTTTGTCAAATGAAAAGGCAGAC TGACAAAAACCAAATAGGATATGGACCCTGTAACAATGATGGAAATAACAATTTTACTTGTACA TTAGTAGATCTCTACTAAATTAATCAATTGGACTGGGTCTTGCTTGTTCATTCCTCTATTGTTT TTGCTTTGAGATTCTTTTTCCCATCATTGCTTTCGACTGAATGGATAGAAATGTCTGATAACAG TTGTATCTGAAAAAAACTGTAACTGCTGATATCTGCGTTTTCTTTACAGAAATCTATTTCAGAC AAGCAAAATACCACTGCCGAAGATTATGCAGCCGGGTCTTCTGAAAGTTCCAAATCATGTGATC AAATAGCATTTAACCCCAATGTCTTCACTGACTTCACATTAGGTGGCAATCAAGAGGTAGGTTA TGTTGCTTATAGGTTATATGTTTTAAGATCATCTCTTAAAATTTATTTAACTGATTGGATGAAT CCTTTTTGGGTTAAACAGGAGATAGCTGCTGATGAAGAAAATGTGAAGAAAGTTAGCTCATACC TTGTGGATGTGGTCCTTCCAAAGTTTATAGAAGATCTTTGCACTCTCGAAGTTTCTCCAATGGA TGGTCAGACTTTGACAGAAGCACTCCATGCTCATGGTGTTAATGTTCGTTACATTGGAAGAGTA AGTTTGTCAGCTGTCGTTATCATTTTGTTAGCTATCTCTATGTTTGAGTTTATTAACAGTAGAT TTGCTCGACCAGGTTGCTAATGGGGTGAAGCATTTGCCTCATTTGTGGGACCTTTGTCTGAATG AGATTACTGTAAGATCCGCAAAGCACATTTTGAAGGTAATTTTGACTGTTGTAAAAGCATGCCA CAACAAGAGTTAGGGTATCTGTGGACACGCTTGTAATAGGTTATAATGTTATTTCTATGTTCTT ACGTCGTTGTGCAGGACATTCTAAGAGATATAGAGGATCACGATATTGGATCAGCAGTCTCACA TTTCCTCAATTGTTTCTTTGGAAACTATCAAACTGCTGGGGGAAAAGCTAGCGCCAACAGCTCT ACTGCCAAAAATCAAAAGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.30966828

Conservation Information
Conserved circRNAs	NA
PMCS	0.30966828

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G52140_circ_g.12

Address

Any questions?

Supported by